Uses of Interface
pal.datatype.MolecularDataType
Packages that use MolecularDataType
Package
Description
Classes dealing with sequence alignments, including methods for reading
and printing in several possible formats, as well as rearranging and
concatenating.
Classes describing data types (nucleotides, amino acids, codons, codon tables etc.)
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Uses of MolecularDataType in pal.alignment
Methods in pal.alignment with parameters of type MolecularDataTypeModifier and TypeMethodDescriptiondouble[]DataTranslator.getFrequencies(MolecularDataType dt, int startingIndex) DataTranslator.toAlignment(MolecularDataType dt, int startingIndex) char[][]DataTranslator.toChars(MolecularDataType dt, int startingIndex) static final int[][]DataTranslator.toNucleotides(int[][] dtStates, MolecularDataType dt) Converts an alignment to a state matrix Stored as [sequnce][site]int[][]DataTranslator.toStates(MolecularDataType dt, int startingIndex) Constructors in pal.alignment with parameters of type MolecularDataTypeModifierConstructorDescriptionDataTranslator(int[][] stateData, MolecularDataType dt) DataTranslator(int[][] stateData, MolecularDataType dt, IdGroup ids) DataTranslator(MolecularDataType dt, char[][] charData) -
Uses of MolecularDataType in pal.datatype
Classes in pal.datatype that implement MolecularDataTypeModifier and TypeClassDescriptionclassimplements DataType for all Codons (including terminators).classimplements a ResidueDataType for GapBalanced notation.classimplements DataType for nucleotides with ambiguous charactersclassimplements DataType for nucleotidesclassimplements a MolecularDataType for amino acids, where we specifiy the Codon Table basis of amino acid by supplying the CodonTable which is/was used for converting Nucleotide sequences to Amino Acids.Methods in pal.datatype that return MolecularDataTypeModifier and TypeMethodDescriptionstatic final MolecularDataTypeMolecularDataType.Utils.getMolecularDataType(DataType dt) Converts (if possible) a DataType into a MolecularDataType.static final MolecularDataTypeDataTypeTool.getNucleotides()A set access point for a data type object describing nucleotides (DNA)static final MolecularDataTypeDataTypeTool.getRNANucleotides()A set access point for a data type object describing nucleotides (RNA)static final MolecularDataTypeDataTypeTool.getUniverisalAminoAcids()A set access point for a data type object describing amino acids (used with relation to the Universal codon table)